I use cn.mops to detect CNVs from WGS data of an haploid genome using the haplocn.mops function . However, I obtain CNVs of copy number 1, which should not be the case since the normal should be 1. I do not get any calls of copy number 2.
Does this function still assume a normal state of 2 despite it being suggested useful for haploid genome?
Would greatly appreciate any clarification on this.